|
| Status |
Public on Jan 25, 2012 |
| Title |
CIN3.2.20 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Cervical tissue, microdissected
|
| Organism |
Homo sapiens |
| Characteristics |
Stage: cervical intraepithelial neoplasia grade 3, prevalent hrHPV infection
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Laser capture microdissection was performed on haematoxylin stained tissue section to obtain the dysplastic cells. Tissues were incubated overnight 37°C in 1M NaSCN. Subsequently, samples were treated with proteinase K for 5 days. DNA was extracted using the DNA Qiagen micro kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
DNA labeling protocol according to Enzo Life Sciences.
|
| |
|
| Channel 2 |
| Source name |
Amplified FFPE cervical DNA from 5 individuals
|
| Organism |
Homo sapiens |
| Characteristics |
Stage: normal cervix
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Laser capture microdissection was performed on haematoxylin stained tissue section to obtain the dysplastic cells. Tissues were incubated overnight 37°C in 1M NaSCN. Subsequently, samples were treated with proteinase K for 5 days. DNA was extracted using the DNA Qiagen micro kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
DNA labeling protocol according to Enzo Life Sciences.
|
| |
|
| |
| Hybridization protocol |
Hybridization protocol available via www.agilent.com
|
| Scan protocol |
Slides were scanned using the Agilent G2505B micro-array scanner. Image data acquisition was performed in feature extraction software v9.5.1 (Agilent Technologies) using the Agilent CGH-v4_95 protocol with default settings
|
| Description |
US22502676_251901510360_S01_CGH_105_Dec08_1_1.txt
Pooled DNA from 5 normal cervical FFPE biopsies was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004
|
| Data processing |
Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104.
The data analysis method used employs across array CGH comparisons (as described in Buffart et al.). In short, using across array CGH it is possible to digitally swap dye channels, allowing one to hybridize 2 different samples to one array and use the reference in another array (either present on the same array slide or even on a different slide) for comparison. Therefore, some of the raw data files are duplicated between Samples, and the appendix (e.g. Cy3_test, Cy3_ref, Cy5_test, Cy5_ref) refers to the label and channel used in each raw data file..
|
| |
|
| Submission date |
Jun 22, 2011 |
| Last update date |
Jan 25, 2012 |
| Contact name |
Daoud Sie |
| E-mail(s) |
d.sie@vumc.nl
|
| Phone |
+31 20 4442428
|
| Organization name |
Vrije Universiteit Medical Center
|
| Department |
Pathology
|
| Lab |
Microarray Core Facility
|
| Street address |
De Boelelaan 1117
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 HV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL8693 |
| Series (1) |
| GSE30155 |
Chromosomal profiles of high-grade cervical intraepithelial neoplasia relate to duration of preceding high-risk human papillomavirus infection |
|
